I'm getting the following error while installing yt-3.2.1 latest release.
Any idea what is going on here?
thanks in advance,
Doing yt update, wiping local changes and updating to branch stable
install_script.sh: line 1025: cd: /home/latif/YT/yt-x86_64/src/yt-hg/: No
such file or directory
copying doc/man/isympy.1 -> /home/latif/YT/yt-x86_64/share/man/man1
Using cached Jinja2-2.8-py2.py3-none-any.whl
Collecting MarkupSafe (from jinja2)
Installing collected packages: MarkupSafe, jinja2
Successfully installed MarkupSafe-0.23 jinja2-2.8
/home/latif/YT/yt-x86_64/bin/python2.7: can't open file 'setup.py': [Errno
2] No such file or directory
Failure. Check /home/latif/YT/yt-x86_64/yt_install.log. The last 10 lines
I've recently been trying to use yt's inline analysis functionality with
Enzo and am having some difficultly getting it to work in parallel. I am
using the development tip of yt. In serial, everything works fine, but in
parallel, I get the following error:
It seems that the issue is that yt is not correctly identifying which grids
are available on a given processory for the EnzoDatasetInMemory object.
Does anyone have an idea of how to fix this? Has anyone else seen this?
For reference, my user_script is just this:
from yt.frontends.enzo.api import EnzoDatasetInMemory
ds = EnzoDatasetInMemory()
ad = ds.all_data()
Thanks for any help,
I followed loosely the example provided here
but encountered an error message using a smoothed covering grid with
SPH data instead of a covering grid. I posted an MWE here:
http://pastebin.com/2sStpLmw which leads to the error message
"AttributeError: 'YTSmoothedCoveringGrid' object has no attribute
I wanted to use a smoothed covering grid because I found that using
SPH data a lot of "holes" are in `covering grid' (but not, e.g., in a
slice plot). So I assumed there is some problem in duplicating the
values from the coarser grids?
My yt version is 3.2-dev.
Thanks a lot for your time & help,
Is there a way to specify the opacity transfer function and the colormap
for volume rendering independently? I am looking for something like
cam.transfer_function.map_to_colormap(), but allowing me to specify a
transfer function for the opacity myself, independently of the transfer
function for the colormap.
What I am trying to achieve with that is the following: a field below a
dynamically chosen cutoff should be completely transparent, so that I
can always see the structure of the field where it is strongest, no
matter what the absolute strength is. The color on the other hand should
depend on the absolute value. E.g. I want to make a movie where I see
the structure of the strongest parts of a field, unobstructed by the
rest, but with a color that changes together with the absolute field
I am trying to assemble Yt volume renderings into a movie using moviepy,
which essentially takes a numpy rgb array for each frame and produces a
However, I am a bit confused on the absolute luminosity in volume
It seems that adding annotations via cam.draw_domain() does not only
draw the domain, but also adjusts the image brightness, which is a bit
surprising. I did not notice that when using cam.save_image() for a
single frame instead using the image array directly, apparently the
former does adjust brightness as well.
I want to avoid rescaling based on average or maximum brightness *of a
single frame* in a movie, because this is misleading.
The brightness of a pixel should only depend on the data along the
corresponding ray, not on the other rays as well. Rather, the scale
should be constant during the movie. I know it is probably difficult,
but is there a way to estimate a reasonable scaling from the expected
data range of the whole evolution and the size of the domain? Also which
other functions besides cam.draw_domain() do implicitly adjust the
I have created a covering grid from a sample Enzo dataset. I would like to write the "density" field to a file. I am doing the following but getting an error.
cg = ds.covering_grid(3,[0.,0.,0.],ds.domain_dimensions*2**2)
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/work/01197/semeraro/maverick/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 399, in write_out
field_data = np.array([self.field_data[field] for field in field_order])
Is it possible to write out the single field to a file from a covering grid?
I've checked, and export_obj() does not work. :(
All of this function collapse in "get_vertex_centered_data"...
I would really appreciate if someone could answer me on the questions I've
sent, since I try to write some code to solve this issue.
Following is the code and errors (python 2.7, YT3.2):
sp = ds.sphere(center=center, radius=(2,'kpc'))
rho = 5e-27
#surf = ds.surface(sp, ('gas', 'density'), rho)
surf = ds.surface(sp, ("deposit", "all_density"), rho)
color_field = "temperature")
yt : [INFO ] 2015-10-18 17:27:05,014 Extracting (sampling: temperature)
Traceback (most recent call
last)<ipython-input-8-9ab0ccc2f049> in <module>() 1
surf.export_obj("sph_2.kpc",----> 2 color_field =
in export_obj(self, filename, transparency, dist_fac, color_field,
emit_field, color_map, color_log, emit_log, plot_index,
color_field_max, color_field_min, emit_field_max, emit_field_min)
1233 if self.vertices is None: 1234 if
color_field is not None:-> 1235
self.get_data(color_field,"face") 1236 elif color_field is
not None: 1237 if color_field not in self.field_data:
in get_data(self, fields, sample_type, no_ghost) 1032
my_verts = self._extract_isocontours_from_grid( 1033
block, self.surface_field, self.field_value,-> 1034
mask, fields, sample_type,
no_ghost=no_ghost) 1035 if fields is not None:
1036 my_verts, svals = my_verts
in _extract_isocontours_from_grid(self, grid, field, value, mask,
sample_values, sample_type, no_ghost) 1053
sample_type = "face", 1054
no_ghost = False):-> 1055 vals =
grid.get_vertex_centered_data(field, no_ghost = no_ghost) 1056
if sample_values is not None: 1057 svals =
in get_vertex_centered_data(self, *args, **kwargs) 443 444
def get_vertex_centered_data(self, *args, **kwargs):--> 445
raise NotImplementedError 446 447 @property
Date: Thu, 15 Oct 2015 08:58:50 -0400
From: "Naiman, Jill" <jill.naiman(a)cfa.harvard.edu>
To: Discussion of the yt analysis package
Subject: Re: [yt-users] surf.export_ply issues
Content-Type: text/plain; charset="utf-8"
One thing you might try is the export_obj function instead of the
export_ply since its been updated more recently. I think it *should* work
on particle data these days (though, someone should correct me if I'm
If that doesn't work, please let the list know though.
On Thu, Oct 15, 2015 at 4:26 AM, Tomer Nussbaum <
> Hello there,
> I want to make a 3D model of my ART simulation with the YT platform. After
> much reading and talking in the YT mirc I understand some code is needed
> make it work.
> I would appreciate if you could answer me about some questions I have had
> through the last couple of days:
> 0. I understand that "export_ply" and the other functions in YTSurfaceBase
> work on other simulation but not on "particle based simulations" like ART.
> is this correct?
> 1. Why does it not work on ART sim?
> 2. What should I do in order to make it run on ART sim?
> 3. What does "get_vertex_centered_data" suppose to do? most of the time
> the error come from this function (not implemented..), is it a the main
> problem? can I work around it?
> 4. Is there a way to transform the ART data to some data that do work in
> order to make it work?
> 5. What is "particle based simulations"?
I am trying to install yt on Pleiades. I was able to complete a number installation steps but I eventually got an error message related to Cython (Cython seems to be installed though). The error message is attached below. Does anybody have an idea what needs to be done to complete this installation?
Dr. Mateusz Ruszkowski
University of Michigan
Department of Astronomy
301C West Hall
1085 South University Ave.
Ann Arbor, MI 48109-1107, USA
e-mail: mateuszr(a)umich.edu <mailto:firstname.lastname@example.org>
% module load pkgsrc/2014Q3
% module load python/2.7.9
% hg clone https://bitbucket.org/yt_analysis/yt <https://bitbucket.org/yt_analysis/yt>
warning: bitbucket.org <http://bitbucket.org/> certificate with fingerprint 46:de:34:e7:9b:18:cd:7f:ae:fd:8b:e3:bc:f4:1a:5e:38:d7:ac:24 not verified (check hostfingerprints or web.cacerts config setting)
destination directory: yt
requesting all changes
adding file changes
added 17568 changesets with 36510 changes to 3053 files (+3 heads)
updating to bookmark @ on branch stable
1209 files updated, 0 files merged, 0 files removed, 0 files unresolved
% cd yt
% hg update yt
317 files updated, 0 files merged, 148 files removed, 0 files unresolved
(leaving bookmark @)
% python setup.py install --user --prefix=/nobackupnfs2/mruszkow
Cython is a build-time requirement for the source tree of yt.
Please either install yt from a provided, release tarball,
or install Cython (version 0.22 or higher).
You may be able to accomplish this by typing:
pip install -U Cython
% pip install -U Cython
Downloading/unpacking Cython from https://pypi.python.org/packages/source/C/Cython/Cython-0.23.4.tar.gz#md5... <https://pypi.python.org/packages/source/C/Cython/Cython-0.23.4.tar.gz#md5...>
Downloading Cython-0.23.4.tar.gz (1.6MB): 1.6MB downloaded
Running setup.py (path:/tmp/pip_build_mruszkow/Cython/setup.py) egg_info for package Cython
Unable to find pgen, not compiling formal grammar.
warning: no files found matching '*.pyx' under directory 'Cython/Debugger/Tests'
warning: no files found matching '*.pxd' under directory 'Cython/Debugger/Tests'
warning: no files found matching '*.h' under directory 'Cython/Debugger/Tests'
warning: no files found matching '*.pxd' under directory 'Cython/Utility'
Installing collected packages: Cython
Found existing installation: Cython 0.21.1
Traceback (most recent call last):
File "/nasa/pkgsrc/2014Q4/lib/python2.7/site-packages/pip/basecommand.py", line 122, in main
status = self.run(options, args)
File "/nasa/pkgsrc/2014Q4/lib/python2.7/site-packages/pip/commands/install.py", line 283, in run
requirement_set.install(install_options, global_options, root=options.root_path)
File "/nasa/pkgsrc/2014Q4/lib/python2.7/site-packages/pip/req.py", line 1431, in install
File "/nasa/pkgsrc/2014Q4/lib/python2.7/site-packages/pip/req.py", line 598, in uninstall
File "/nasa/pkgsrc/2014Q4/lib/python2.7/site-packages/pip/req.py", line 1836, in remove
File "/nasa/pkgsrc/2014Q4/lib/python2.7/site-packages/pip/util.py", line 295, in renames
File "/nasa/pkgsrc/2014Q4/lib/python2.7/shutil.py", line 300, in move
File "/nasa/pkgsrc/2014Q4/lib/python2.7/shutil.py", line 247, in rmtree
rmtree(fullname, ignore_errors, onerror)
File "/nasa/pkgsrc/2014Q4/lib/python2.7/shutil.py", line 252, in rmtree
onerror(os.remove, fullname, sys.exc_info())
File "/nasa/pkgsrc/2014Q4/lib/python2.7/shutil.py", line 250, in rmtree
OSError: [Errno 30] Read-only file system: '/nasa/pkgsrc/2014Q4/lib/python2.7/site-packages/Cython/Build/BuildExecutable.py'
Storing debug log for failure in /u/mruszkow/.pip/pip.log
I’m working on accessing the information stored by a phase plot in plot.profile.field_data, but yt recognizes this as a list, so I can’t seem to get the information out of this list to use.
I’ve attached the script with how I’ve been attempting to access the data (http://paste.yt-project.org/show/5985/ <http://paste.yt-project.org/show/5985/>), and then the output and various procedures I’ve tried (http://paste.yt-project.org/show/5986/ <http://paste.yt-project.org/show/5986/>).
I’ve been working on a MacBook Pro, OS X 10.10.5, with yt version 3.2 (installed using miniconda, so no changeset).
I appreciate any help you might be able to give me.
Astrophysics | Lyman Briggs College
Women’s & Gender Studies | College of Arts & Letters
LGBTQ and Sexuality Studies Specialization
Women in Science, President
Undergraduate Teaching Assistant
Department of Physics and Astronomy
Michigan State University